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@@ -18,12 +18,12 @@
2. [SIMULATING EXPERIMENTS FROM THE 2015 pairSEQ PAPER](#simulating-experiments-from-the-2015-pairseq-paper)
1. [EXPERIMENT 1](#experiment-1)
2. [EXPERIMENT 3](#experiment-3)
6. [TODO](#todo)
7. [CITATIONS](#citations)
8. [EXTERNAL LIBRARIES USED](#external-libraries-used)
9. [ACKNOWLEDGEMENTS](#acknowledgements)
10. [AUTHOR](#author)
11. [DISCLOSURE](#disclosure)
6. [CITATIONS](#citations)
7. [EXTERNAL LIBRARIES USED](#external-libraries-used)
8. [ACKNOWLEDGEMENTS](#acknowledgements)
9. [AUTHOR](#author)
10. [DISCLOSURE](#disclosure)
11. [TODO](#todo)
## ABOUT
@@ -593,6 +593,37 @@ underlying frequency distribution drastically affect the results. The real distr
than the simulated exponential distribution. Implementing a way to exert finer control over the sampling distribution from
the file of distinct cells may enable better simulated replication of this experiment.
## CITATIONS
* Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)
* Duan, R., Su H. ["A Scaling Algorithm for Maximum Weight Matching in Bipartite Graphs."](https://web.eecs.umich.edu/~pettie/matching/Duan-Su-scaling-bipartite-matching.pdf) Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms, p. 1413-1424. (2012)
* Melhorn, K., Näher, St. [The LEDA Platform of Combinatorial and Geometric Computing.](https://people.mpi-inf.mpg.de/~mehlhorn/LEDAbook.html) Cambridge University Press. Chapter 7, Graph Algorithms; p. 132-162 (1999)
* Fredman, M., Tarjan, R. ["Fibonacci heaps and their uses in improved network optimization algorithms."](https://www.cl.cam.ac.uk/teaching/1011/AlgorithII/1987-FredmanTar-fibonacci.pdf) J. ACM, 34(3):596–615 (1987))
* Bertsekas, D., Castañon, D. ["A forward/reverse auction algorithm for asymmetric assignment problems."](https://www.mit.edu/~dimitrib/For_Rev_Asym_Auction.pdf) Computational Optimization and Applications 1, 277-297 (1992)
* Dimitrios Michail, Joris Kinable, Barak Naveh, and John V. Sichi. ["JGraphT—A Java Library for Graph Data Structures and Algorithms."](https://dl.acm.org/doi/10.1145/3381449) ACM Trans. Math. Softw. 46, 2, Article 16 (2020)
## EXTERNAL LIBRARIES USED
* [JGraphT](https://jgrapht.org) -- Graph theory data structures and algorithms
* [JHeaps](https://www.jheaps.org) -- For pairing heap priority queue used in maximum weight matching algorithm
* [Apache Commons CSV](https://commons.apache.org/proper/commons-csv/) -- For CSV file output
* [Apache Commons CLI](https://commons.apache.org/proper/commons-cli/) -- To enable command line arguments for scripting.
## ACKNOWLEDGEMENTS
BiGpairSEQ was conceived in collaboration with the author's spouse, Dr. Alice MacQueen, who brought the original
pairSEQ paper to the author's attention and explained all the biology terms he didn't know.
## AUTHOR
BiGpairSEQ algorithm and simulation by Eugene Fischer, 2021. Improvements and documentation, 2022–2025.
## DISCLOSURE
The earliest versions of the BiGpairSEQ simulator were written in 2021 to let Dr. MacQueen test hypothetical extensions
of the published pairSEQ protocol while she was interviewing for a position at Adaptive Biotechnologies. She was
employed at Adaptive Biotechnologies starting in 2022.
The author has worked on this BiGpairSEQ simulator since 2021 without Dr. MacQueen's involvement, since she has had
access to related, proprietary technologies. The author has had no such access, relying exclusively on the 2015 pairSEQ
paper and other academic publications. He continues to work on the BiGpairSEQ simulator recreationally, as it has been
a means of exploring some very beautiful math.
## TODO
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
@@ -645,35 +676,3 @@ the file of distinct cells may enable better simulated replication of this exper
* Should probably refactor to use apache commons rng for this
* Use commons JCS for caching
* Parameterize pre-filtering options
## CITATIONS
* Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)
* Duan, R., Su H. ["A Scaling Algorithm for Maximum Weight Matching in Bipartite Graphs."](https://web.eecs.umich.edu/~pettie/matching/Duan-Su-scaling-bipartite-matching.pdf) Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms, p. 1413-1424. (2012)
* Melhorn, K., Näher, St. [The LEDA Platform of Combinatorial and Geometric Computing.](https://people.mpi-inf.mpg.de/~mehlhorn/LEDAbook.html) Cambridge University Press. Chapter 7, Graph Algorithms; p. 132-162 (1999)
* Fredman, M., Tarjan, R. ["Fibonacci heaps and their uses in improved network optimization algorithms."](https://www.cl.cam.ac.uk/teaching/1011/AlgorithII/1987-FredmanTar-fibonacci.pdf) J. ACM, 34(3):596–615 (1987))
* Bertsekas, D., Castañon, D. ["A forward/reverse auction algorithm for asymmetric assignment problems."](https://www.mit.edu/~dimitrib/For_Rev_Asym_Auction.pdf) Computational Optimization and Applications 1, 277-297 (1992)
* Dimitrios Michail, Joris Kinable, Barak Naveh, and John V. Sichi. ["JGraphT—A Java Library for Graph Data Structures and Algorithms."](https://dl.acm.org/doi/10.1145/3381449) ACM Trans. Math. Softw. 46, 2, Article 16 (2020)
## EXTERNAL LIBRARIES USED
* [JGraphT](https://jgrapht.org) -- Graph theory data structures and algorithms
* [JHeaps](https://www.jheaps.org) -- For pairing heap priority queue used in maximum weight matching algorithm
* [Apache Commons CSV](https://commons.apache.org/proper/commons-csv/) -- For CSV file output
* [Apache Commons CLI](https://commons.apache.org/proper/commons-cli/) -- To enable command line arguments for scripting.
## ACKNOWLEDGEMENTS
BiGpairSEQ was conceived in collaboration with the author's spouse, Dr. Alice MacQueen, who brought the original
pairSEQ paper to the author's attention and explained all the biology terms he didn't know.
## AUTHOR
BiGpairSEQ algorithm and simulation by Eugene Fischer, 2021. Improvements and documentation, 2022–2023.
## DISCLOSURE
The earliest versions of the BiGpairSEQ simulator were written in 2021 to let Dr. MacQueen test hypothetical extensions
of the published pairSEQ protocol while she was interviewing for a position at Adaptive Biotechnologies. She has been
employed at Adaptive Biotechnologies since 2022.
The author has worked on this BiGpairSEQ simulator since 2021 without Dr. MacQueen's involvement, since she has had
access to related, proprietary technologies. The author has had no such access, relying exclusively on the 2015 pairSEQ
paper and other academic publications. He continues to work on BiGpairSEQ
recreationally, as it involves some very beautiful math.